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used in CLI .set_footer()

The callback could perhaps be avoided. See #3292.

See #2739.

See #2739.

Should be explicit due to the callback

I finally understood how to use CLI11 callbacks.
See https://cliutils.gitlab.io/CLI11Tutorial/chapters/advanced-topics.html

Close #2749.

See #3292.

Closes #2741.

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

A boolean parameter has been added in the Germline constructors in order to
check if the automaton needs to be constructed or not.
For example with -Z all, the automaton is not constructed.

For more informations see #3268

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

The FineSegmenter constructor handles the filtering of the germline. By default
the value is "NO_LIMIT_VALUE", which means the filtering isn't active.

For more informations about it #3268.

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

In #3268 we want to add a specific command-line option for the filtering.
The -Z has only been declared in the getopt. The remaining task is to
check if -Z still has NO_LIMIT_VALUE as an argument. If so the automaton
is not built, otherwise the automaton is built and the argument is used to
filter the BioReader.

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

For the purpose of adding the -Z option (described in #3264), the -H option
will show its description.

Mathieu Giraud authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

Incidentally close #3271.

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

(squashed from earlier commits)

set_index() keeps track of the number of germlines refeering to it.
This is necessary so that the last germline destructor can actually
delete the index.

Memory is correctly free-ed with a return, while it is not with an exit.
Valgrind will thus complain when terminating the program with an exit()
this won't be the case with a return.

When calling exit() the memory allocated by the system is not
properly free-ed. This is not really a problem in itself but
Valgrind will complain about that.

There are two solutions:
1. replace exit() with return, but this
   requires to be in the main() function
2. prevent Valgrind from being used in
   other cases (exit because of an error)

See #3031

Some allocations were not properly free-ed.
Spotted by Valgrind.

See #3031

See #2635.

See #2635.

See #2247 and #3010.

See #3011.

The break is useless here as usage() does an exit()
but this will avoid gcc complaints.

See #2247 and #2916.